Stream: implementers
Topic: Genetic data: Exomiser results to FHIR
Marta Herranz (Oct 20 2020 at 10:14):
Hi! I am doing a genetic data mapping and would like to know if anyone has worked with this before.
After running exomiser (https://exomiser.github.io/Exomiser/) with a set of symptoms and VCF files I get the gene information for a particular case. In this result I have data from:
- Gene identifier
- Mode of inheritance
- Some scores: combined, phenotype and variant.
- Contributing variants: chromosome, position, ref and alt, frequency data, variant effect, clinVar data (alleleId, interpretations, reviewStatus), etc.
From what I have read so far, the genetic information is stored in "Observation" resources: http://hl7.org/fhir/observation-genetic.html. And that this also has several extensions that I could use.
Would I have to map all my values by hand or does anyone know if there is anything I can use to automate it?
With all the observation resources created for a patient, then I would have to create a "DiagnosticReport-genetics Profile" resource that points to all of the above, is that right?
Thank you very much!
Lloyd McKenzie (Oct 20 2020 at 15:30):
You should look at the genomics reporting IG
Lloyd McKenzie (Oct 20 2020 at 15:30):
You might also want to track the discussions on this stream: #genomics
Marta Herranz (Oct 20 2020 at 15:38):
Thank you very much for your response @Lloyd McKenzie ! I have continued to investigate and have found the following:
How can I save the genetic information in VCF format I can use this converter to go to FHIR: https://github.com/openelimu/VCF-2-FHIR
I have not been able to use it well yet because of the formats of the files, but as soon as I have it I will update it here in case someone finds it useful.
If someone has already used it with Exomiser and can tell me how they have done it I would appreciate it.
Lloyd McKenzie (Oct 20 2020 at 15:40):
I would post related questions under the #genomics stream - the folks there are more likely to be able to help.
Marta Herranz (Oct 20 2020 at 15:46):
Perfect, thank you very much @Lloyd McKenzie ! I'm new here and I don't really know how it all works yet.
Lloyd McKenzie (Oct 20 2020 at 16:14):
No worries - and welcome :)
Last updated: Apr 12 2022 at 19:14 UTC
